Cd40 CD40 antigen [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cd40provided by MGI
Official Full Name: CD40 antigenprovided by MGI
Primary source: MGI:MGI:88336
See related: Ensembl:ENSMUSG00000017652 AllianceGenome:MGI:88336
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: IGM; p50; Bp50; GP39; IMD3; TRAP; HIGM1; T-BAM; Tnfrsf5
Summary: Predicted to enable antigen binding activity; protein domain specific binding activity; and ubiquitin protein ligase binding activity. Involved in B cell mediated immunity; CD40 signaling pathway; and intracellular calcium ion homeostasis. Acts upstream of or within several processes, including defense response to other organism; phosphatidylinositol 3-kinase/protein kinase B signal transduction; and positive regulation of B cell activation. Located in external side of plasma membrane and intracellular membrane-bounded organelle. Part of CD40 receptor complex. Is expressed in several structures, including alimentary system; brain; hemolymphoid system gland; limb; and reproductive system. Human ortholog(s) of this gene implicated in several diseases, including Kawasaki disease; autoimmune disease (multiple); end stage renal disease; hyperimmunoglobulin syndrome (multiple); and non-Hodgkin lymphoma (multiple). Orthologous to human CD40 (CD40 molecule). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Broad expression in spleen adult (RPKM 16.5), lung adult (RPKM 9.0) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 H3; 2 85.38 cM

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (164897535..164913574)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (165055614..165071654)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

IFNgamma insufficiency during mouse intra-vaginal Chlamydia trachomatis infection exacerbates alternative activation in macrophages with compromised CD40 functions.
Title: IFNγ insufficiency during mouse intra-vaginal Chlamydia trachomatis infection exacerbates alternative activation in macrophages with compromised CD40 functions.
TRAF6 and TRAF2/3 Binding Motifs in CD40 Differentially Regulate B Cell Function in T-Dependent Antibody Responses and Dendritic Cell Function in Experimental Autoimmune Encephalomyelitis.
Title: TRAF6 and TRAF2/3 Binding Motifs in CD40 Differentially Regulate B Cell Function in T-Dependent Antibody Responses and Dendritic Cell Function in Experimental Autoimmune Encephalomyelitis.
CD40-CD40 ligand interaction between periodontal ligament cells and cementoblasts enhances periodontal tissue remodeling in response to mechanical stress.
Title: CD40-CD40 ligand interaction between periodontal ligament cells and cementoblasts enhances periodontal tissue remodeling in response to mechanical stress.
Importance of CD40/CD40 dyad in the course of infection with Trypanosoma cruzi: Impact of its inhibition.
Title: Importance of CD40/CD40 dyad in the course of infection with Trypanosoma cruzi: Impact of its inhibition.
Myeloid CD40 deficiency reduces atherosclerosis by impairing macrophages' transition into a pro-inflammatory state.
Title: Myeloid CD40 deficiency reduces atherosclerosis by impairing macrophages' transition into a pro-inflammatory state.
Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer's disease.
Title: Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer's disease.
Inhibition of CD40-TRAF6-dependent inflammatory activity halts the onset of diabetic retinopathy in streptozotocin-diabetic mice.
Title: Inhibition of CD40-TRAF6-dependent inflammatory activity halts the onset of diabetic retinopathy in streptozotocin-diabetic mice.
Effector memory CD4(+) T cells induce damaging innate inflammation and autoimmune pathology by engaging CD40 and TNFR on myeloid cells.
Title: Effector memory CD4(+) T cells induce damaging innate inflammation and autoimmune pathology by engaging CD40 and TNFR on myeloid cells.
Deficiency of Endothelial CD40 Induces a Stable Plaque Phenotype and Limits Inflammatory Cell Recruitment to Atherosclerotic Lesions in Mice.
Title: Deficiency of Endothelial CD40 Induces a Stable Plaque Phenotype and Limits Inflammatory Cell Recruitment to Atherosclerotic Lesions in Mice.
The Role of CD40 in Allergic Rhinitis and Airway Remodelling.
Title: The Role of CD40 in Allergic Rhinitis and Airway Remodelling.

Submit: New GeneRIF Correction See all GeneRIFs (274)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (2)
Endonuclease-mediated (10) 1 citation
Targeted (8) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Tnfrsf5 (e-PCR), detects polymorphism
- UniSTS:144657

AI326936 (e-PCR)
- UniSTS:178770

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables antigen binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in B cell activation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within B cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in B cell activation	ISO Inferred from Sequence Orthology more info
involved_in B cell mediated immunity	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of B cell proliferation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of B cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in CD40 signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in CD40 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway via JAK-STAT	IEA Inferred from Electronic Annotation more info
involved_in cellular response to mechanical stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within defense response to protozoan	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within defense response to virus	IDA Inferred from Direct Assay more info	PubMed
involved_in immune response-regulating cell surface receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within immune response-regulating cell surface receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in immunoglobulin production	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of interleukin-12 production	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular calcium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular calcium ion homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within phosphatidylinositol 3-kinase/protein kinase B signal transduction	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of B cell proliferation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of B cell proliferation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of GTPase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MAP kinase activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MAPK cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of NF-kappaB transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of blood vessel endothelial cell migration	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of blood vessel endothelial cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of endothelial cell apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of endothelial cell apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of interleukin-12 production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of interleukin-4-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of isotype switching to IgG isotypes	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein kinase C signaling	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein kinase C signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tyrosine phosphorylation of STAT protein	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of immune response	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of immunoglobulin production	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of CD40 receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of CD40 receptor complex	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in external side of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in varicosity	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tumor necrosis factor receptor superfamily member 5

Names: B-cell surface antigen CD40; CD40L receptor; T-cell differentiation antigen

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_011611.3 → NP_035741.2 tumor necrosis factor receptor superfamily member 5 isoform 1 precursor

See identical proteins and their annotated locations for NP_035741.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AL591411, AL591495

Consensus CDS

CCDS17069.1

UniProtKB/Swiss-Prot

P27512, Q3TS33, Q3TSL2, Q3U799, Q3U7C9, Q3UBH3, Q542B1, Q8K2X6, Q99NE0, Q99NE1, Q99NE2, Q99NE3

Related

ENSMUSP00000017799.6, ENSMUST00000017799.12

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
NM_170702.3 → NP_733803.2 tumor necrosis factor receptor superfamily member 5 isoform 5 precursor

See identical proteins and their annotated locations for NP_733803.2

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (5), also known as type V, lacks an internal segment near the C-terminus, compared to isoform 1.

Source sequence(s)

AL591411, AL591495

Consensus CDS

CCDS17070.1

UniProtKB/Swiss-Prot

P27512

Related

ENSMUSP00000073386.3, ENSMUST00000073707.9

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40
NM_170703.3 → NP_733804.1 tumor necrosis factor receptor superfamily member 5 isoform 2 precursor

See identical proteins and their annotated locations for NP_733804.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The resulting isoform (2), also known as type II, lacks an internal segment near the C-terminus, compared to isoform 1.

Source sequence(s)

AL591411, AL591495

Consensus CDS

CCDS17071.1

UniProtKB/Swiss-Prot

P27512

Related

ENSMUSP00000080059.5, ENSMUST00000081310.11

Conserved Domains (2) summary

cd00185
Location:62 → 103

TNFRSF; CRD2 [structural motif]

cl22855
Location:26 → 166

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
NM_170704.3 → NP_733805.1 tumor necrosis factor receptor superfamily member 5 isoform 4 precursor

See identical proteins and their annotated locations for NP_733805.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 3' coding region that results in a frameshift, compared to variant 1. The resulting isoform (4), also known as type IV, has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

AL591411, AL591495

UniProtKB/Swiss-Prot

P27512

Related

ENSMUSP00000139193.2, ENSMUST00000184221.2

Conserved Domains (1) summary

cd13407
Location:26 → 186

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40

RNA

NR_027852.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) retains an intron, compared to variant 1. This variant is represented as non-coding because it is a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL591411, AL591495

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

164897535..164913574

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006499155.5 → XP_006499218.1 tumor necrosis factor receptor superfamily member 5 isoform X2

Conserved Domains (2) summary

cd00185
Location:15 → 55

TNFRSF; CRD4 [structural motif]

cl22855
Location:1 → 55

TNFRSF; Tumor necrosis factor receptor superfamily (TNFRSF)
XM_006499154.4 → XP_006499217.1 tumor necrosis factor receptor superfamily member 5 isoform X1

Conserved Domains (1) summary

cd13407
Location:26 → 166

TNFRSF5; Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40